DIA-Umpire

DIA-Umpire converts data independent acquisition (DIA) mass spectrometry proteomics data into pseudo-tandem mass spectrometry (MS) spectra and extracts precursor- and fragment-ion quantification for database-search-based peptide and protein identification.

Key Features:

• Pseudo-Tandem MS Spectra Assembly: Detects and assembles precursor and fragment chromatographic features into pseudo-tandem mass spectrometry (MS) spectra for identification with conventional database-searching and protein-inference tools.
• Untargeted Peptide and Protein Identification: Performs untargeted peptide and protein identification from DIA data using conventional database-searching and protein-inference tools without reliance on a spectral library.
• Quantification via Precursor- and Fragment-Ion Intensities: Quantifies analytes using both precursor- and fragment-ion intensities to provide peptide- and protein-level quantitative measurements.
• Targeted Extraction for Consistent Quantification: Performs targeted extraction of quantitative information based on peptides initially identified in only a subset of samples to improve consistency across multiple samples.

Scientific Applications:

• Glycoproteomics: Demonstrated on publicly available glycoproteomics datasets to handle modified peptide analyses.
• Affinity Purification–Mass Spectrometry (AP-MS): Applied to AP-MS datasets to support identification and quantification in interaction studies.
• Complex Sample Analysis: Validated using control samples of varying complexity to assess performance across diverse proteomic conditions.

Methodology:

Detects and assembles precursor and fragment chromatographic features into pseudo-tandem MS spectra; enables identification by conventional database-searching and protein-inference tools without a spectral library; quantifies by precursor- and fragment-ion intensities; and performs targeted extraction of quantitative information for peptides identified in a subset of samples.